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Syngene InGenius3 Manual

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  • Page 2: Table Of Contents

    Contents Chapter One- Introduction..................Applications supported..............Hardware..................1.2.1 Specifications................... 1.2.2 System Components.................. 1.2.2.1 Darkroom..................1.2.2.2 UV transilluminator................1.2.2.3 Filter Draw..................1.2.3 Accessories..................1.2.3.1 Visible Light Converter..............1.2.3.2 Blue LED transilluminator..............1.2.3.3 Thermal Printer................1.2.3.4 Analysis Software..................1.2.4 Set-up....................1.2.4.1 Installing GeneSys Image Capture Software........1.2.4.2 Minimum system requirements............
  • Page 3 Image Rotation................Image Source................Saturation Button................Enhancement Tools..............3D view..................View Images screen..............Browse Images screen..............Chapter Five- Configurations................Saving Configurations..............5.1.1 Saving Configurations in Autocapture mode........ 5.1.2 Saving Configurations in Manual mode........5.1.3 Opening Configurations..............Chapter Six- Troubleshooting and General Information........ Technical Information..............

  • Page 4: Chapter One- Introduction

    1. Introduction Chapter One- Introduction The InGenius system supports multiple applications including DNA/RNA gel imaging such as EtBr, SYBR Gold and UltraSafe Blue and visible stained gels i.e. coomassie blue and silver stain. The InGenius gel imaging system is a dedicated UV transilluminator-based system with a small footprint.

  • Page 5: System Components

    1. Introduction 1.2.2 System components 1.2.2.1 Darkroom The darkroom has a sliding door. The darkroom features:  Slide out mid wave 302nm UV transilluminator  Internal LED white light  Safety switch to protect from accidental UV exposure InGenius manual March 2012...

  • Page 6: Uv Transilluminator

    Interchange a range of filters for extensive choice of fluorescent applications. 1.2.3 Accessories 1.2.3.1 Visible light converter Syngene offer a visible light converter that can be placed on top of the UV transilluminator for imaging coomassie and silver stained gels. 1.2.3.2 Blue LED transilluminator...

  • Page 7: Analysis Software

    The drivers will automatically install. 1.2.3.4 Analysis software The InGenius system is supplied with a copy of GeneTools analysis software from Syngene. This may be loaded on a PC of your choice. Please see the loading instructions within the CD cover. 1.2.4 Set-up Please refer to the Installation quick guide on how to set up the camera and darkroom.

  • Page 8: Software Installation

    1. Introduction 1.2.4.3 Software Installation This section provides information regarding the installation of GeneSys image capture software. You will need to install the software from an account that has Administrator rights. Installation is performed in the following sequence 1. Hardware Information 2.

  • Page 9: Select Destination Location

    1. Introduction Now enter your specific model from the list then click ‘Next’ 1.2.4.5 Select Destination Location Please select the folder in which you would like GeneSys to be installed. Select Browse to explore more folder options. Click ‘Next’ InGenius manual March 2012...

  • Page 10: Select Start Menu Folder

    1. Introduction 1.2.4.6 Select Start Menu Folder Please select where you would like to create the shortcuts for the program. To select a different folder click the browse button. Click ‘Next’. The software is now ready to install. Click ‘Install’ to continue the Installation process.

  • Page 11: Device Driver Installation Wizard

    1. Introduction 1.2.4.7 Device Driver Installation Wizard This wizard will now install the software drivers that some computer devices need in order to complete the installation. Click ‘Next’. Click ’Finish’ to complete the Device Driver Installation Wizard. Enabling secure user accounts To enable a secure user account you must use your Microsoft Windows account log in.

  • Page 12: Setting Up Hardware

    1. Introduction Figure 1- Hardware page You can select your preferences on the type of report settings that you would like. You can select to view or print the full report (Image, File description and capture properties) or the basic report (image and capture settings). To change the settings of the printer use this icon.
  • Page 13 1. Introduction Figure 2- User Preferences page InGenius manual March 2012...

  • Page 14: Chapter Two- Auto Capture And Manual Image Acquisition

    2. Auto Capture and Manual Image Acquisition Chapter Two- Auto Capture and Manual Image Acquisition Auto Capture The basis of auto capture mode is a series of steps that form a structured workflow. The workflow is very easy to navigate through by using the green bouncing arrow present in the bottom right hand corner of the screen to move forward to the next screen (Figure 3).

  • Page 15: Capture Screen

    2. Auto Capture and Manual Image Acquisition 2.0.5 Capture screen The capture screen offers a wide range of functions including the ability to save, print, edit images and analyse the captured image (GeneTools is required). The captured image appears in the main window with the summary of the protocol used present on the right hand side.
  • Page 16 2. Auto Capture and Manual Image Acquisition Step Four As a default setting GeneSys shows you the best imaging condition for your hardware set-up. To see more options check the ‘ More Options’ box. To view the non-UV protocols check the ‘Non-UV protocols only’ box. Step Five Place your sample on top of the transilluminator and close the door.

  • Page 17: Other White Light Image

    2. Auto Capture and Manual Image Acquisition Capturing an Image of a protein gel (coomassie, silver stained) or other white light image (colony plate, autorad, microtitre plate etc.) Step One Select Auto Capture from the home screen. Step Two From the Sample Selection screen select the following Gel as Sample Format, the sample type is Protein and then select that your gel is visibly stained.
  • Page 18 2. Auto Capture and Manual Image Acquisition Step Four As a default setting GeneSys shows you the best imaging condition for your hardware set-up. Step Five If you have a white light converter then place your sample on top of the converter then place the converter on top of the transilluminator and close the door.
  • Page 19 2. Auto Capture and Manual Image Acquisition To ensure that the image you are capturing is not saturated select the ‘Show Saturation button’ (Figure 5). Saturation will only show when the slider bars have been moved to each end of the brightness/contrast slider. Over-exposed (saturated) white bands will show red and over-exposed black areas in blue (Figure 6).

  • Page 20: Manual Capture

    2. Auto Capture and Manual Image Acquisition Depending on which type of sample (UV, epi lights or transilluminator white light) you would like to neutral field you may get either of the bottom two messages shown below. Figure 8- Neutral Fielding Dialog boxes To freeze the image press (if you have a touch screen monitor) or click the Capture button (Figure 9).
  • Page 21 2. Auto Capture and Manual Image Acquisition Once Manual capture has been selected the camera is live. To be able to position your sample the appropriate lighting and filter combination need to be selected. Both the lighting and filter menus have a drop-down menu where you can select from all the available lighting and filters present in your system (Figure 10).
  • Page 22 2. Auto Capture and Manual Image Acquisition (saturated) white bands will show red and over-exposed black areas in blue (Figure 14). Figure 13- Show Saturation button Figure 14- Image of a gel showing saturation The bands coloured red show that these bands are saturated GeneSys software also has the ability to Neutral field.
  • Page 23 2. Auto Capture and Manual Image Acquisition Figure 16- Neutral Fielding Dialog boxes To freeze the image press (if you have a touch screen monitor) or click the Capture button (Figure 17). The image is no longer Live. If you wish to abort capture you can press the ‘Stop’...
  • Page 24 2. Auto Capture and Manual Image Acquisition The histogram tool is very useful for illustrating the distribution of grey scales within the image (Figure 19). The level of grey scales produced is dependant on exposure time - up to 65536 grey scales will be displayed (Figure 20). Figure 19- Manual Histogram tool button Figure 20- Graphical representation of the number of greyscale levels captured...
  • Page 25 2. Auto Capture and Manual Image Acquisition Figure 22- Image Information Icon GeneSys software can be used to set up custom protocols containing system settings (lighting, filter and camera settings) which can be repeated and retrieved at any time. These repeatable custom protocols are configurations, to save a configuration select the following icon (refer to chapter 5 for more information on how to set up a configuration).

  • Page 26: Chapter Three-Exporting, Saving And Printing Images

    A dialog box will pop up where you can enter a file name for your image. You can also use the ‘Save as type’ drop down menu and select to save the image as a SynGene Data (*sgd), TIFF image file (*tif), Windows Bitmap image file (*bmp) or a JPEG image file (*jpg) (Figure 28).

  • Page 27: Saving Annotations

    3. Exporting, Saving and Printing Images The default is set to SynGene Data (*.sgd) which is a secure file and GLP compliant. These files can only be opened or altered in Syngene software packages such as GeneTools. SGD files contain all the capture information such as lighting, filter, exposure times and many more complex details i.e.

  • Page 28: Exporting Images To Genetools Analysis Software

    Figure 31- Print preview Exporting Images to GeneTools analysis software Various file formats can be exported from GeneSys to GeneTools. Syngene recommends uncompressed TIFF or .sgd to maintain quantification. To export a captured or saved image simply select the ‘open selected images in GeneTools’...

  • Page 29: Chapter Four- Browse, Edit And View Screens

    4. Browse, Edit and View Screens Chapter Four- Browse, Edit and View Screens Edit screen The Edit screen offers a variety of functions ranging from image enhancement and 3D view to changing the resolution of the image for publication purposes (Figure 33).

  • Page 30: Annotation Tools

    4. Browse, Edit and View Screens Annotation tools There are several annotation tools currently available with GeneSys software. The annotation tools will appear automatically when you enter the Edit screen to access the Enhancement and 3D tools you will need to select the appropriate icon (Figure 35).
  • Page 31 4. Browse, Edit and View Screens This tool can be used when you wish to draw a filled shape. Press the Fill button then select the shape you wish to draw from the icons shown in figure 36. To draw rectangles, circles, freehand shapes, lines and arrows click the appropriate icon shown below (Figure 36).

  • Page 32: Image Rotation

    4. Browse, Edit and View Screens Any annotations made will be automatically saved when images are in SGD format. When saving in other formats, you must check the engrave box to ensure annotations are saved. See section 3.1 for more information on saving images. To save any annotation that you have made to your image in a separate file that can be re-opened over another image, press on (touchscreen) or click the following icon (Figure 38).

  • Page 33: Saturation Button

    4. Browse, Edit and View Screens .(Figure 41a). To go back to the processed image press the processed image button (Figure 41b) Figure 41- Image source icons a) Original image and b) Processed image Saturation button To show saturation move the slider bars to each end of the brightness/contrast slider.

  • Page 34: View

    4. Browse, Edit and View Screens Click on this icon to apply a sharpening filter to your image. When this filter has been applied band edges should become more pronounced but you may also observe an increase in the graininess of the image. Click on this icon to apply a smoothing filter.
  • Page 35 4. Browse, Edit and View Screens Figure 44- 3D View screen To control the view use the following controls Figure 45- 3D View controls Use the blue circles to rotate the image and the green arrows to move the image left to right and up and down the screen.
  • Page 36 4. Browse, Edit and View Screens Adding a false colour wash can improve the contrast. Select the ‘Default’ button and from the menu select the colour wash you wish to apply to the 3D image (Figure 47). The colour wash button can also be used to emulate different dyes, select the green colour wash to emulate a SYBR Green DNA gel, the yellow colour wash imitates a SYBR Gold DNA gel.

  • Page 37: View Images Screen

    4. Browse, Edit and View Screens The selected image(s) can then be saved, printed, sent to the View screen for comparison or to the Edit screen for further enhancement (Figure 49). Figure 49- Save, print, view and edit image icons a) Save icon, b) print icon, c) View images icon and d) Edit screen icon Single images can be sent to GeneTools for analysis (Figure 50).
  • Page 38 4. Browse, Edit and View Screens Figure 51- View Images Screen The zoom slider can be used to increase or decrease the size of the image (Figure 52). Figure 52- View Screen digital zoom slider bar The View images screen also enables you to compare up to four images. To compare images simply highlight the images you wish to compare then select the icon with the magnifying glass (Figure 53).
  • Page 39 4. Browse, Edit and View Screens Figure 54- Change Layout Screen The default setting is set to link all images that are being compared allowing the zoom and brightness and contrast all images to be altered to the same degree (Figure 55).

  • Page 40: Browse Images Screen

    4. Browse, Edit and View Screens to alter under the Link heading (Figure 56). To link images again select the linked chains icon (Figure 56). Figure 56- Linking and Unlinking images The key identifies which image you have selected and the position of each of the images that you are comparing (Figure 57).
  • Page 41 4. Browse, Edit and View Screens Figure 59- Browse screen InGenius manual March 2012...

  • Page 42: Chapter Five- Configurations

    5. Configurations Chapter Five- Configurations GeneSys software can be used to run specific applications with repeatable workflows and to design custom configurations with a wide variety of settings that are easily accessable, adaptable and re-usable at any time. Saving Configurations 5.1.1 Saving configurations in Auto Capture mode Set up your Protocol by working through the following screens Sample selection, Dye selection, Protocol selection and Sample positioning.

  • Page 43: Saving Configurations In Manual Mode

    5. Configurations You can also modify an existing protocol by selecting the configuration you wish to edit from the ‘Save Configuration’ dialog box. 5.1.2 Saving Configurations in Manual mode Once you have selected the lighting and filter options you wish to use, position your sample so it is zoomed in and in focus then capture the image.

  • Page 44: Chapter Six- Troubleshooting And General Information

    If your dye/reagent is not listed then please contact support@syngene.com Technical Information GeneSys software hardware installation guide Please visit the Syngene website www.syngene.com to download the following technical literature (This is also available on your GeneSys software CD). Quick Guides...

  • Page 45: Troubleshooting

    Contact database support@syngene.com Dye name is greyed out have Contact appropriate hardware ‘support@syngene.com’ to image that particular dye upgrade your system Check the ‘hardware list’ on Programme in any extra the hardware screen lights or filters that you may have...

  • Page 46: Glossary

    6. Glossary Glossary The following glossary defines words used in this manual. Auto Capture- the software will configure the optimal exposure time for your sample using the maximum number of greyscales from your camera. Binning- is a process that further enhances the sensitivity of the CCD sensor in terms of speed of the image acquistion.

  • Page 47: Index

    Index Index 3D View 26, 31,34 Binning 20,43 Annotation Tools Browse Images 34,37 Autocapture 12,14 Capture screen 11,12,22,33 Destination location 5 Change Layout 35,36,37 Device Driver Installation Wizard 5,8 Colour Wash 33 Dye Selection 12,14 Configurations 8,22,39,49 Edit 12,26,27,33,34,38,40 Filters 3,18,42 Enabling secure user accounts Flip (horizontal/vertical) 30,31...
  • Page 48 Index Manual capture 11,17,21 Navigation arrow Multi select mode Neutral Fielding 16,17,1920,43 Opening User Configurations 40 Protocol Selection 11,39 Print 9,12,23,24,25,34 Quick guides Recent selections only 12,14 Reversal icon Rotation 1,29 Sample selection 11,12,14,39 Technical Information 58 Sample positioning 11,13,15,39,40 Troubleshooting Save 12,15,23,34,39,40...
  • Page 49 Index User configurations 40 View available hardware View Images 34,35,38 Workflow status bar Zoom 13,15,21,35,36 Zoom and range slider bars InGenius manual March 2012...

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